chr10-88657742-G-T

Variant names:

• chr10-88657742-G-T
• rs701826

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.291 in 150,996 control chromosomes in the GnomAD database, including 6,716 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.291 AC: 43955 AN: 150876 Hom.: 6712 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.300

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.291 AC: 43981 AN: 150996 Hom.: 6716 Cov.: 31 AF XY: 0.295 AC XY: 21723 AN XY: 73628

African (AFR) AF: 0.253 AC: 10411 AN: 41070

American (AMR) AF: 0.359 AC: 5446 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2751 AN: 5138

South Asian (SAS) AF: 0.359 AC: 1713 AN: 4778

European-Finnish (FIN) AF: 0.251 AC: 2573 AN: 10262

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19087 AN: 67788

Other (OTH) AF: 0.305 AC: 642 AN: 2108

Alfa AF: 0.269 Hom.: 2253

Bravo AF: 0.295

Asia WGS AF: 0.456 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.66
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs701826; hg19: chr10-90417499;